The Open-Specimen Movement

Abstract

The open-science movement seeks to increase transparency, reproducibility, and access to scientific data. As primary data, preserved biological specimens represent records of global biodiversity critical to research, conservation, national security, and public health. However, a recent decrease in specimen preservation in public biorepositories is a major barrier to open biological science. As such, there is an urgent need for a cultural shift in the life sciences that normalizes specimen deposition in museum collections. Museums embody an open-science ethos and provide long-term research infrastructure through curation, data management and security, and community-wide access to samples and data, thereby ensuring scientific reproducibility and extension. We propose that a paradigm shift from specimen ownership to specimen stewardship can be achieved through increased open-data requirements among scientific journals and institutional requirements for specimen deposition by funding and permitting agencies, and through explicit integration of specimens into existing data management plan guidelines and annual reporting.

The critical importance of vouchers in genomics

“…We surveyed the NCBI list of vertebrate genomes (focusing on reference/representative genomes of each species) with an assembly publication date up to January 1, 2020 ( https://www.ncbi.nlm.nih.gov/genome/browse#!/eukaryotes/vertebrates ) and coverage of 30X or greater. Although we focused on reviewing vertebrate genomes, the lack of vouchers is a problem among genetic sequences submitted from many different types of organisms ( Leray et al, 2019 ; Pleijel et al, 2008 ; Peterson et al, 2007 ; Lendemer et al, 2020 ; Colella et al, 2021 ; Schoch et al, 2020 ; Thompson et al, 2021 ; Beaz-Hidalgo et al, 2015 ; Chakrabarty, 2010 ; Chakrabarty et al, 2013 ). When available, we also cross-checked the original publications reporting genome assemblies for references to a deposited voucher specimen.…”

“…Where possible, having a proper voucher can be evidence that collections of rare or endangered species were made legally ( Colella et al, 2021 ). Data associated with vouchers typically includes links to permits, field notes, and other associated documentation; without a specimen these documents are often lost because they are not associated with museums or other long-term archival research collections ( Simmons, 2017 ).…”

“…Although there are several important components of the vouchering process, taxonomic identification of voucher specimens is critical because proper identification is required to understand and contextualize all aspects of biology pertinent to a species ( Colella et al, 2021 ). Taxonomy in most biological disciplines is based on morphological and genetic divergence ( Schoch et al, 2020 ), and joint archiving of both data types is essential to verifying the identity of biological materials now and in the future.…”

Leveraging natural history biorepositories as a global, decentralized, pathogen surveillance network

“…Wildlife sampling of leaf-nosed bats in Ghana recently identified a wild reservoir of rubella, a viral disease whose origins and natural reservoirs had remained unknown for >100 years after emerging in humans [ 32 ]. Genetic screening of wildlife in China recently identified horseshoe bats as a potential reservoir for SARS-CoV-2 [ 33 , 34 ]; however, in this case, a paucity of open-access voucher specimens has hindered expanded host screening and limited investigation into the ecology, evolution, and environmental associations of seropositive samples, leaving SARS-CoV-2 emergence a global mystery [ 4 , 35 – 36 ].…”

“…The global scale of EIDs, exemplified by the current SARS-CoV-2 pandemic, calls for an intentional shift away from current reactive responses to EIDs, toward more proactive models that encourage early detection, identification, monitoring, and prevention (e.g., Documentation, Assessment, Monitoring, Action [DAMA] protocol [ 6 , 49 ]; Fig 1 ), possible by expanding One Health approaches to include the Global Museum [ 23 – 28 ]. To this end, we must invest in expanded biorepository capacity, quality, and expertise to meet the needs of EID research, an approach to building infrastructure that has not yet been normalized across disciplines [ 4 – 5 ].…”